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- PDB-7ezn: Crystal structure of CnYvh1 complex with vanadate -

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Basic information

Entry
Database: PDB / ID: 7ezn
TitleCrystal structure of CnYvh1 complex with vanadate
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / DUSP / phosphatase / inhibitor
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
VANADATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChoi, M.K. / Yoo, Y.
Citation
Journal: To Be Published
Title: Crystal structure of CnYvh1 complex with vanadate
Authors: Choi, M.K. / Yoo, Y.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2014
Title: The family-wide structure and function of human dual-specificity protein phosphatases.
Authors: Jeong, D.G. / Wei, C.H. / Ku, B. / Jeon, T.J. / Chien, P.N. / Kim, J.K. / Park, S.Y. / Hwang, H.S. / Ryu, S.Y. / Park, H. / Kim, D.S. / Kim, S.J. / Ryu, S.E.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9323
Polymers22,7551
Non-polymers1772
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-3 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.194, 66.194, 120.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-575-

HOH

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Components

#1: Protein Protein-tyrosine-phosphatase


Mass: 22754.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_01203 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VTB5, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M Magnesium chloride, 0.08 M Tris-HCl pH 8.5, 24 % (w/v) PEG 4000, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→33.1 Å / Num. obs: 24183 / % possible obs: 94.58 % / Redundancy: 2 % / Biso Wilson estimate: 29.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01125 / Net I/σ(I): 33.71
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.2128 / Num. unique obs: 1709 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ki9

4ki9


Resolution: 1.8→33.1 Å / SU ML: 0.1345 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1800 7.45 %
Rwork0.2001 22368 -
obs0.2008 24168 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 9 76 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851404
X-RAY DIFFRACTIONf_angle_d1.54491900
X-RAY DIFFRACTIONf_chiral_restr0.0718212
X-RAY DIFFRACTIONf_plane_restr0.0062244
X-RAY DIFFRACTIONf_dihedral_angle_d13.397524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.2371960.25321187X-RAY DIFFRACTION66.89
1.85-1.90.2281110.23371382X-RAY DIFFRACTION77.28
1.9-1.960.27371270.22831577X-RAY DIFFRACTION89.17
1.96-2.030.27441430.23081774X-RAY DIFFRACTION99.22
2.03-2.120.25371430.2111782X-RAY DIFFRACTION99.33
2.12-2.210.20571430.21741792X-RAY DIFFRACTION99.69
2.21-2.330.23551440.21771780X-RAY DIFFRACTION99.64
2.33-2.470.2141460.21221802X-RAY DIFFRACTION99.85
2.48-2.670.24071430.23041806X-RAY DIFFRACTION99.85
2.67-2.930.21881490.21361843X-RAY DIFFRACTION99.95
2.93-3.360.20811480.22041830X-RAY DIFFRACTION99.95
3.36-4.230.19271490.17381861X-RAY DIFFRACTION99.75
4.23-33.10.17721580.17411952X-RAY DIFFRACTION98.14

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